Found some more info about the class lights and other lights (form the old Atlas Forum):
Marker lights were installed on some rebuilds in the late 1990’s in place of the class lights next to the number boards. At other times the train was run with the headlight on dim if markers were not installed.
Those lights to the sides of the number boards were class lights, I believe they were still required when the F-40 was first delivered in 1976. The Center Red Light was an emergency strobe which was activated when the train was placed in emergency. In the late 1990’s the Xenon Strobes were removed as they were no longer required due to the installation of Ditch lights.
So it really depends on what year you want your F40 to be. If it is pre-ditch lights, they you need the roof Xenon Strobes. The lights to the side of the number boards would be class lights and not yet changed out to red marker lights.
However if you are in the ditch light era…1990s and up…then the roof strobes would be removed and the class lights might be changed to red markers.
Oh you mentioned you already added the ditch lights, so no strobes and maybe red markers if you want.